alison van eenennaam, ph.d. · • semen • hair • tissue mmi genomics $24 (1-19 samples) $22...
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Van Eenennaam 2009 Animal Biotechnology and Genomics Education
“What has DNA done for me lately?”
Alison Van Eenennaam, Ph.D. Cooperative Extension Specialist
Animal Biotechnology and Genomics UC Davis [email protected]
http://animalscience.ucdavis.edu/animalbiotech/
Van Eenennaam 2009
Curly Calf: What is Arthrogryposis Multiplex (AM) ??
Curly calf syndrome
Since September 8, 2008, researchers at the University of Illinois have been investigating the genetic condition called Arthrogryposis Multiplex (AM), commonly referred to as “Curly Calf Syndrome (CCS)” in Angus cattle.
Van Eenennaam 2009
Arthrogryposis Multiplex (curly calf)
Calves are born dead or die shortly after birth. The spine and legs appear crooked or twisted and the joints of the legs are often fixed in positions. Front legs are contracted and rear limbs may be contracted or extended. Calves are small and appear thin due to limited muscle development. There may be a cleft affecting the nose or palate.
Appearance of a calf with Arthrogryposis Multiplex. Photo used with permission from http://www.angus.org.
Van Eenennaam 2009
AM (Curly Calf Syndrome) is caused by a recessive genetic defect, tentatively traced to a maternal grandsire “Rito 9J9 of B156 7T26, Registration No. 9682589”, of GAR Precision 1680 (USA1680).
The “impacted genetics” therefore currently refers to all animals with Rito 9J9 of B156 7T26 in their pedigrees.
A list of AM Free (AMF) and carrier (AMC) bulls and cows can be found at the Angus association website
http://www.angus.org/ccs_info.html
DNA test has been developed for Arthrogryposis Multiplex (curly calf)
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Other genetic abnormalities to be on the look out for:
Lethal Congenital Hydrocephalus: Born near term, 25-35 lb birth weights, head is volleyball to basketball sized Fawn Calf Syndrome: calves at birth assume an abnormal crouched posture, resembling an elk or deer fawn
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Companies offering AM (curly calf) test
DNA
testing
company
Website Cost of test Preferred
tissue type
Agri-
genomics
www.agrigenomicsinc.com $25 • Whole blood
• Semen
Igenity www.igenity.com $26 • Whole blood
• Semen
• Hair
• Tissue
MMI
genomics
www.metamorphixinc.com $24 (1-19 samples)
$22 (20-99 samples)
$20 (100 + samples)
• Semen
• Blood on FTA cards
Pfizer
Animal
Genetics
www.pfizeranimalgenetics.com $29*
(*each test earns $10
credit towards
GeneSTAR testing
through 6/1/09)
• Whole blood
• Semen
• Blood on FTA cards
• Hair sample
(> 25 hairs)
Animal Biotechnology and Genomics Education Van Eenennaam 2009
The following groups also collaborate with GeneSeek, Inc., to collect and provide samples for AM testing (~$25/sample)
Stockman's Resource Center LLC 2371 330th Street Eddyville, Iowa 52553 [email protected] www.stockmansresource.com Office phone: 641-969-4111 Mobile: 641-660-0771
Genex Cooperative, Inc. Headquarters: 100 MBC Drive Shawano, WI 54166 Phone: 888-333-1783 Fax: 715-526-3219 [email protected]
SEK Genetics Don Coover 9525 70th Rd. Galesburg, KS 66740 [email protected] Phone: 800-443-6389
Van Eenennaam 2009
From September 8–November 3, 2008 identified genetic problem, developed test prototype, and released carrier status of 736 AI bulls!
From a scientific standpoint, the AM test is based on the presence of a specific change or mutation in the DNA sequence. For AM, this change is the complete deletion of a segment of DNA that encompasses two different genes (a gene is a sequence in the DNA that encodes a protein).
One of these genes is expressed at a crucial time in the development of nerve and muscle tissue. The mutation results in no protein being produced from this gene and therefore it is unable to carry out its normal function, referred to as a loss-of-function mutation.
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Why are these genetic defects appearing now?
Naturally-occurring recessive genetic defects are common in all species, and only become evident when certain lines of cattle are used very heavily, such that both cows and bulls have common ancestors in their pedigree, (double bred descendants) thereby allowing a rare genetic defect to become homozygous in their offspring
Animal Biotechnology and Genomics Education Van Eenennaam 2009
The bovine genome is similar in size to the genomes of humans, with an estimated size of 3 billion base pairs.
Human & cattle genomes are 83% identical
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Loss of Myostatin gene causes double muscling
Van Eenennaam 2009
Genotyping
TTGAA
TTTAA
TTGAA TTTAA
½ ½
Carrier bull - AMC
Animal Biotechnology and Genomics Education Van Eenennaam 2009
AMC x AMC = ¼ affected (AMA): ½ normal-appearing carrier (AMC): ¼ AM free (AMF)
If only one parent is a carrier, then all of the offspring will be normal appearing, but half of them will be carriers (AMC)
AMC x AMF = ½ normal-appearing carrier (AMC): ½ AM free calf (AMF)
Breeding two carriers will give 25% chance of affected calf
Animal Biotechnology and Genomics Education Van Eenennaam 2009 Van Eenennaam 2009 Animal Biotechnology and Genomics Education
There will be a Quiz! DNA-test Opinion Survey
Alison Van Eenennaam, UC Davis
Cooperative Extension Specialist
Animal Biotechnology and Genomics
University of California, Davis
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Kitten is to cat as calf is to _ _ .
tiger
cow
lion
bear
2% 2%2%
94%1. tiger
2. cow
3. lion
4. bear
Animal Biotechnology and Genomics Education Van Eenennaam 2009
This is a picture
of D _ A.
B N C L
4%0%
4%
92%
1. B
2. N
3. C
4. L
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who are you?
SEEDSTOCK
COM
MERCIA
L
ALLIED
OTHER
NONE
12%
72%
4%10%
2%
1. Seedstock producer
2. Commercial producer
3. Allied industry
4. Other
5. None
Animal Biotechnology and Genomics Education Van Eenennaam 2009
How many cows do you run?
0 <
50
50-1
00
100-2
00
200-5
00
500-1
000
>1000
12%
18%
12%
6%
14%
20%
18%1. 0
2. <50
3. 50-100
4. 100-200
5. 200-500
6. 500-1000
7. >1000
Animal Biotechnology and Genomics Education Van Eenennaam 2009
How many bulls do you plan to purchase this year?
0 1
-2 3
-5 6
-10
>10
19%
49%
2%
6%
23%
1. 0
2. 1-2
3. 3-5
4. 6-10
5. >10
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who has heard about DNA testing for beef cattle?
I hav
e
I hav
e not
10%
90%1. I have
2. I have not
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who has collected samples from their cattle for DNA testing?
Yes
I ha
ve
Not m
e
68%
32%
1. Yes I have
2. Not me
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Current applications: Tests for simple traits
Testing for genetic defects e.g. curly calf
Testing for single gene traits
Testing for Coat color
Testing for horned/polled
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who has tested their cattle for simple traits?
Yes
I hav
e N
o
77%
23% Examples • Horned/Polled • Coat color • Genetic defects
1. Yes I have
2. No
Animal Biotechnology and Genomics Education Van Eenennaam 2009
If you breed a curly calf carrier cow (AMC) to an curly calf free bull (AMF), what is the chance that the offspring will be stillborn
as a result of being curly calf?
0
¼ (2
5%)
½ (5
0%)
2/3
(66%)
¾ (
75%)
1 (
100%)
51%
34%
0%2%
0%
13%
1. 0
2. ¼ (25%)
3. ½ (50%)
4. 2/3 (66%)
5. ¾ (75%)
6. 1 (100%)
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Current applications: Paternity testing
Identify bulls producing problem calves
Identify extremes in phenotypes
ID of cleanup bulls after AI
Determine bull dominance – 50% of the bulls sire 80% of the calves
Enable on-ranch EPD calculations for commercial sires in a herd
Animal Biotechnology and Genomics Education Van Eenennaam 2009
UC Davis herd 2006
Animal Biotechnology and Genomics Education Van Eenennaam 2009
UC Davis herd 2007
Animal Biotechnology and Genomics Education Van Eenennaam 2009
UC Davis herd 2008
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Meat Tenderness
Quality Grade (Marbling)
Beef Cattle Feed Efficiency
Yield Grade
Fat thickness
Ribeye area
Average Daily Gain
(Heifer pregnancy rate, stayability, calving ease, docility)
Tests for complex traits – currently 10-100 SNPs
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Results reported as # of stars/MVP
Results reported on scale 1-10
Results reported as “MGV”
GeneSTAR Quality Grade
Igenity Profile – Quality Grade
Tru-Marbling
GeneSTAR Tenderness
Igenity Profile - Tenderness
Tru-Tenderness
Feed Efficiency Igenity Profile – Marbling, Yield Grade, Fat thickness, Ribeye area, Average Daily Gain, Heifer pregnancy rate, stayability, calving ease, docility
Pfizer Igenity MMI
Quality Grade
Tenderness
Other
Current applications: Test for complex traits
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who has tested their cattle for complex (multigenic) traits?
Yes
I hav
e N
o
82%
18%
1. Yes I have
2. No
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Which quantitative tests have you done?
Quality
Gra
de
Ten
dernes
s
Fee
d Effi
ciency
Som
e of t
hese
All
of thes
e
Oth
er
None
5%0% 0%
74%
2%
17%
2%
1. Marbling/Quality grade
2. Tenderness
3. Feed Efficiency
4. Some of the above
5. All of the above
6. Other
7. None
Animal Biotechnology and Genomics Education Van Eenennaam 2009
What test did you use?
Gen
e Sta
r
Igen
ity
MM
I gen
omic
s
Lep
tin
More
than
1
Oth
er
Don
’t re
call
Non
e
3% 3% 3%
77%
9%
0%
6%
0%
1. Gene Star/Bovigen/Pfizer
2. Igenity Profile/Merial
3. MMI genomics (TruTenderness/TruMarbling)
4. Leptin
5. More than 1 of the above
6. Other
7. Don’t recall which test
8. None
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Who thinks they might use DNA testing for complex traits one day?
Alrea
dy do
May
be
Unlik
ely
NEVE
R!!
19%
10%13%
58%1. Already do
2. Maybe
3. Unlikely
4. NEVER!!
Animal Biotechnology and Genomics Education Van Eenennaam 2009
How much would you be willing to pay for a marbling test...
$0 $5 $10 $20 $50 $100 >$100
25%
34%
18%
0%0%
9%
14%
1. $0
2. $5
3. $10
4. $20
5. $50
6. $100
7. >$100
Animal Biotechnology and Genomics Education Van Eenennaam 2009
How much would you be willing to pay for a tenderness test?
$0 $5 $10 $20 $50 $50-
100
>$100
33%
67%
0% 0%0%0%0%
1. $0
2. $5
3. $10
4. $20
5. $50
6. $50-100
7. >$100
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Is there a value to increasing the accuracy of EPDs?
Yes
No
7%
93%1. Yes
2. No
Animal Biotechnology and Genomics Education Van Eenennaam 2009
What is the value of accuracy?
Animal Biotechnology and Genomics Education Van Eenennaam 2009
For which trait would an increase in accuracy have the greatest value?
CED
BW
WW
YW
SC
Mar
bling
Ten
ders
Fee
d Eff.
7%
9%
22%
36%
2%
11%
4%
9%
1. CED
2. BW
3. WW
4. YW
5. SC
6. Marbling
7. Tenderness
8. Feed Efficiency
Animal Biotechnology and Genomics Education Van Eenennaam 2009
If there was a DNA test for weaning
weight –would you use it?
Yes
No
22%
78%1. Yes
2. No
Animal Biotechnology and Genomics Education Van Eenennaam 2009
How much would you pay for a DNA test that increases the accuracy of a yearling bull WW EPD from 0.05 (i.e. parent average) to 0.4?
$0 $1-10 $20-50 $50-100 $100-200 $200-500 >$500
5%
68%
17%
5%
0%2%2%
1. $0
2. $1-10
3. $20-50
4. $50-100
5. $ 100-200
6. $200-500
7. >$500
Animal Biotechnology and Genomics Education Van Eenennaam 2009
That is equivalent to having 22 progeny records at birth
Number of progeny records required BIF accuracy Low heritability (0.1) Moderate heritability (0.3)
.01 1 1
.02 2 1
.05 4 2
.08 8 3
.13 13 5
.20 22 7
.29 38 12
.40 70 22
.56 167 53
.93 1921 608
.99 3800 1225
Animal Biotechnology and Genomics Education Van Eenennaam 2009
$0 $1-10 $20-50 $50-100 $100-200 $200-500 >$500
0%
27%
33%
13%
0%
7%
20%
How much would you pay for a DNA test that increases the accuracy of a yearling bull WW EPD from 0.05 (i.e. parent average) to 0.4?
1. $0
2. $1-10
3. $20-50
4. $50-100
5. $ 100-200
6. $200-500
7. >$500
Animal Biotechnology and Genomics Education Van Eenennaam 2009
$0 $10-50 $50-100 $100-200 $200-500 $500-
1000
>$1000
2%
63%
16%
5%2%
5%7%
How much would you pay for a DNA test that increases the accuracy of a yearling bull WW EPD from 0.05 (i.e. parent average) to 0.9?
1. $0
2. $10-50
3. $50-100
4. $100-200
5. $ 200-500
6. $500-1000
7. >$1000
Animal Biotechnology and Genomics Education Van Eenennaam 2009
California to host BIF 2009! Mark your calendars!
http://www.calcattlemen.org/bif2009.html
Animal Biotechnology and Genomics Education Van Eenennaam 2009
-30.0
-20.0
-10.0
0.0
10.0
20.0
30.0
10 20 30 40 50 60 70
AAA EPD
2006-2
007 E
PD
208
2006: 13
calves
2007: 9
357
2006: 1 calf
2007: 6
calves
Animal Biotechnology and Genomics Education Van Eenennaam 2009
Questions ?